Variant report

Variant	rs6680541
Chromosome Location	chr1:180949780-180949781
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:180927440..180930124-chr1:180947176..180950127,2	MCF-7	breast:
2	chr1:180948731..180951492-chr1:181058649..181061974,3	MCF-7	breast:
3	chr1:180948321..180949844-chr1:180950401..180952045,2	K562	blood:
4	chr1:180949324..180951935-chr1:180953444..180956382,3	K562	blood:
5	chr1:180944502..180946802-chr1:180948049..180950056,2	MCF-7	breast:
6	chr1:180949324..180952994-chr1:180953444..180956382,4	K562	blood:

Variant related genes	Relation type
ENSG00000272198	Chromatin interaction
ENSG00000243155	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1044595	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10753232	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11586493	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12744212	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12754041	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1411478	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2331903	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3747957	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3789362	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3789364	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4111520	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4495657	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4652545	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4652547	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4652548	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59145927	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6425657	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6425658	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6665134	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7516739	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7528526	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7543927	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7553330	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014404	chr1:180770155-181090200	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
2	esv3342865	chr1:180933678-181018012	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	esv3383831	chr1:180937224-181029755	Strong transcription Active TSS Weak transcription Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180923600-180958800	Weak transcription	Small Intestine	intestine
2	chr1:180929000-180956200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:180930200-180950200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
4	chr1:180931600-180950800	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr1:180933400-180974600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr1:180937800-180950200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr1:180937800-180950400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr1:180938600-180950600	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr1:180939000-180950000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr1:180939200-180950600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr1:180939200-180950600	Strong transcription	Primary B cells from cord blood	blood
12	chr1:180939200-180954400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr1:180939200-180965600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr1:180940400-180988400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr1:180941800-180950600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr1:180943000-180957400	Weak transcription	Fetal Heart	heart
17	chr1:180943600-180955600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr1:180943600-180972000	Weak transcription	Psoas Muscle	Psoas
19	chr1:180943600-180979800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr1:180944400-180962600	Strong transcription	Osteobl	bone
21	chr1:180944600-180951600	Strong transcription	Hela-S3	cervix
22	chr1:180944600-180957600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr1:180944800-180952600	Strong transcription	A549	lung
24	chr1:180944800-180970800	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr1:180945400-180950200	Strong transcription	Primary T cells fromperipheralblood	blood
26	chr1:180945400-180950600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr1:180945400-180950600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr1:180945400-180975000	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr1:180945600-180951000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr1:180945600-180951400	Weak transcription	Colon Smooth Muscle	Colon
31	chr1:180945600-180974800	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr1:180945800-180950000	Weak transcription	Gastric	stomach
33	chr1:180945800-180950600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr1:180945800-180956200	Weak transcription	Colonic Mucosa	Colon
35	chr1:180946000-180950000	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr1:180946000-180950000	Weak transcription	NHDF-Ad	bronchial
37	chr1:180946000-180952200	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr1:180946000-180953800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr1:180946200-180949800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr1:180946200-180950000	Weak transcription	Rectal Smooth Muscle	rectum
41	chr1:180946200-180950200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr1:180946200-180950600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr1:180946200-180954600	Weak transcription	NHLF	lung
44	chr1:180946400-180950000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr1:180946400-180951200	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr1:180946600-180950000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr1:180946600-180950000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr1:180946600-180950000	Weak transcription	Right Ventricle	heart
49	chr1:180946600-180950200	Weak transcription	Lung	lung
50	chr1:180946600-180952000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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